Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HDAC3

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
prostate tumor
cell line
LNCaP
treatment
pGIPZ
antibody
HDAC3, Abcam, ab7030, GR3202599-3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified. ChIP-seq libraries were prepared from 3-5ng ChIPped DNA by using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer's instructions. Postamplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

Sequencing Platform

instrument_model
Illumina HiScanSQ

hg38

Number of total reads
12027559
Reads aligned (%)
90.3
Duplicates removed (%)
22.3
Number of peaks
2258 (qval < 1E-05)

hg19

Number of total reads
12027559
Reads aligned (%)
89.6
Duplicates removed (%)
22.5
Number of peaks
2140 (qval < 1E-05)

Base call quality data from DBCLS SRA